Vectors and Matrices

Tcl does not handle mathematical expressions very well. It is slow at
evaluating expressions, and provides no facility for handling vectors
or matrices. Since the latter two are needed for structure analysis,
we have added routines to manipulate them.

A vector in VMD is a list of numbers. All of the vector routines
but one will work with vectors of any length; veccross will only
use vectors of three numbers. A matrix is a 4x4 collection of numbers
stored as a list of 4 vectors of 4 numbers, in row-major order.

Following are descriptions and examples of all the commands. For more
examples of vectors, though without much documentation, the script
used to test the vectors implementation is located at $env(VMDDIR)/scripts/vmd/test-vectors.tcl.

Since Tcl is slow at math, some of these commands have been
reimplemented in C++. (The original definition is in the vmd script
distribution, but it is redefined later on inside VMD). At times,
the speedup is a factor of 40 or more. These commands are noted by
(C++).